Speaking in Strasbourg on Tuesday, Juncker said, "In truth it has pained me to spend so much of this mandate dealing with Brexit when I have thought of nothing less than how this union could better do for its citizens - waste of time and waste of energy."
He was updating members on last week’s summit in Brussels where a deal was agreed between the EU and UK.
Juncker said the European Parliament could only approve the Brexit deal that was struck with London last week once it has been approved by the British Parliament.
"We need now to watch events in Westminster very closely, but it’s not possible, not imaginable that this Parliament would ratify the agreement before Westminster has ratified the agreement. First London, then Brussels and Strasbourg,” he said.
Juncker said it had disappointed him that he could not have spent more of his five-year mandate on making the EU serve its citizens better.
Also on Tuesday in the same debate, Council President Donald Tusk told members, "I have no doubt we should treat the UK request for an extension in all seriousness."
"It has pained me to spend so much of this mandate dealing with Brexit ... waste of time and waste of energy" Jean-Claude Juncker
Tusk added, "The European Parliament has a role to play, and it is an important one. The situation is quite complex following events over the weekend in the UK, and the British request for an extension of the Article 50 process."
"I am consulting the leaders on how to react, and will decide in the coming days. It is obvious that the result of these consultations will very much depend on what the British Parliament decides, or doesn’t decide. We should be ready for every scenario."
"But one thing must be clear: as I said to Prime Minister Johnson on Saturday, a no-deal Brexit will never be our decision."